Starting phenix.real_space_refine on Thu Mar 5 17:16:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lwi_23546/03_2026/7lwi_23546.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lwi_23546/03_2026/7lwi_23546.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lwi_23546/03_2026/7lwi_23546.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lwi_23546/03_2026/7lwi_23546.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lwi_23546/03_2026/7lwi_23546.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lwi_23546/03_2026/7lwi_23546.map" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.068 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 15204 2.51 5 N 3924 2.21 5 O 4614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23847 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7809 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 47, 'TRANS': 953} Chain breaks: 7 Chain: "B" Number of atoms: 7809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7809 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 47, 'TRANS': 953} Chain breaks: 7 Chain: "C" Number of atoms: 7809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7809 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 47, 'TRANS': 953} Chain breaks: 7 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 5.43, per 1000 atoms: 0.23 Number of scatterers: 23847 At special positions: 0 Unit cell: (132.556, 133.625, 173.178, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 4614 8.00 N 3924 7.00 C 15204 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=1.96 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.02 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.00 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 603 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG A1310 " - " ASN A 165 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 603 " " NAG B1303 " - " ASN B 61 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 122 " " NAG B1306 " - " ASN B 282 " " NAG B1307 " - " ASN B 165 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 165 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C 122 " Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 1.1 seconds 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5622 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 54 sheets defined 27.8% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 197 through 200 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.685A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.065A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.530A pdb=" N LEU A 387 " --> pdb=" O SER A 383 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 383 through 388' Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.963A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.731A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.560A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.825A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.714A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.598A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.650A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.738A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.889A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 753 Processing helix chain 'B' and resid 754 through 757 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.609A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.658A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.549A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.983A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.708A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.572A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.373A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 344 removed outlier: 3.523A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.805A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.844A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.717A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.960A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.812A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.854A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.506A pdb=" N ASN C 907 " --> pdb=" O ALA C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.514A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 986 through 1033 removed outlier: 4.147A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1127 through 1129 No H-bonds generated for 'chain 'C' and resid 1127 through 1129' Processing helix chain 'C' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.858A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.925A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR C 572 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.925A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR C 572 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.830A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.364A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.712A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.418A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL A 595 " --> pdb=" O SER A 316 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.728A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 538 through 543 removed outlier: 5.126A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.424A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.281A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB9, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.273A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1081 through 1082 removed outlier: 4.673A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC3, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.776A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.001A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.658A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.371A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.439A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.212A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.621A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.212A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.621A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.870A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.416A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD7, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD8, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.304A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.520A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.812A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE3, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.105A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.861A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.041A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.577A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.743A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.932A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP C 398 " --> pdb=" O VAL C 512 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.715A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.635A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AF5, first strand: chain 'C' and resid 718 through 722 Processing sheet with id=AF6, first strand: chain 'C' and resid 718 through 722 removed outlier: 3.570A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.462A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 5.482A pdb=" N VAL C1122 " --> pdb=" O PHE C1089 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N PHE C1089 " --> pdb=" O VAL C1122 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N GLY C1124 " --> pdb=" O ALA C1087 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 1094 through 1097 1049 hydrogen bonds defined for protein. 2835 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.95 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6385 1.33 - 1.46: 4518 1.46 - 1.58: 13334 1.58 - 1.70: 0 1.70 - 1.82: 129 Bond restraints: 24366 Sorted by residual: bond pdb=" CA PRO B 862 " pdb=" C PRO B 862 " ideal model delta sigma weight residual 1.517 1.543 -0.026 6.70e-03 2.23e+04 1.55e+01 bond pdb=" C5 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.413 1.491 -0.078 2.00e-02 2.50e+03 1.54e+01 bond pdb=" C5 NAG C1310 " pdb=" O5 NAG C1310 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C5 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C5 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.413 1.487 -0.074 2.00e-02 2.50e+03 1.38e+01 ... (remaining 24361 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 20831 1.55 - 3.09: 9437 3.09 - 4.64: 2546 4.64 - 6.19: 293 6.19 - 7.73: 37 Bond angle restraints: 33144 Sorted by residual: angle pdb=" CA PHE B 347 " pdb=" CB PHE B 347 " pdb=" CG PHE B 347 " ideal model delta sigma weight residual 113.80 120.11 -6.31 1.00e+00 1.00e+00 3.98e+01 angle pdb=" CA ASN C 165 " pdb=" CB ASN C 165 " pdb=" CG ASN C 165 " ideal model delta sigma weight residual 112.60 106.74 5.86 1.00e+00 1.00e+00 3.43e+01 angle pdb=" CA PHE A 643 " pdb=" CB PHE A 643 " pdb=" CG PHE A 643 " ideal model delta sigma weight residual 113.80 119.49 -5.69 1.00e+00 1.00e+00 3.24e+01 angle pdb=" CA ASP C 796 " pdb=" CB ASP C 796 " pdb=" CG ASP C 796 " ideal model delta sigma weight residual 112.60 117.95 -5.35 1.00e+00 1.00e+00 2.86e+01 angle pdb=" CA PHE B 643 " pdb=" CB PHE B 643 " pdb=" CG PHE B 643 " ideal model delta sigma weight residual 113.80 119.13 -5.33 1.00e+00 1.00e+00 2.84e+01 ... (remaining 33139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 13853 17.79 - 35.58: 829 35.58 - 53.37: 125 53.37 - 71.17: 72 71.17 - 88.96: 28 Dihedral angle restraints: 14907 sinusoidal: 6180 harmonic: 8727 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -167.84 81.84 1 1.00e+01 1.00e-02 8.24e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual 93.00 155.08 -62.08 1 1.00e+01 1.00e-02 5.10e+01 dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual 93.00 149.19 -56.19 1 1.00e+01 1.00e-02 4.26e+01 ... (remaining 14904 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2277 0.081 - 0.163: 1325 0.163 - 0.244: 228 0.244 - 0.326: 42 0.326 - 0.407: 4 Chirality restraints: 3876 Sorted by residual: chirality pdb=" CA ASP A 571 " pdb=" N ASP A 571 " pdb=" C ASP A 571 " pdb=" CB ASP A 571 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.14e+00 chirality pdb=" CA GLU A 773 " pdb=" N GLU A 773 " pdb=" C GLU A 773 " pdb=" CB GLU A 773 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CA ALA A 123 " pdb=" N ALA A 123 " pdb=" C ALA A 123 " pdb=" CB ALA A 123 " both_signs ideal model delta sigma weight residual False 2.48 2.13 0.36 2.00e-01 2.50e+01 3.18e+00 ... (remaining 3873 not shown) Planarity restraints: 4281 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 165 " -0.144 2.00e-02 2.50e+03 1.50e-01 2.82e+02 pdb=" CG ASN C 165 " 0.090 2.00e-02 2.50e+03 pdb=" OD1 ASN C 165 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN C 165 " 0.227 2.00e-02 2.50e+03 pdb=" C1 NAG C1307 " -0.180 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C1074 " 0.139 2.00e-02 2.50e+03 1.48e-01 2.73e+02 pdb=" CG ASN C1074 " -0.078 2.00e-02 2.50e+03 pdb=" OD1 ASN C1074 " -0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN C1074 " -0.227 2.00e-02 2.50e+03 pdb=" C1 NAG C1305 " 0.179 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 28 " 0.202 2.00e-02 2.50e+03 1.13e-01 2.53e+02 pdb=" CG TYR B 28 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TYR B 28 " -0.089 2.00e-02 2.50e+03 pdb=" CD2 TYR B 28 " -0.088 2.00e-02 2.50e+03 pdb=" CE1 TYR B 28 " -0.068 2.00e-02 2.50e+03 pdb=" CE2 TYR B 28 " -0.070 2.00e-02 2.50e+03 pdb=" CZ TYR B 28 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR B 28 " 0.179 2.00e-02 2.50e+03 ... (remaining 4278 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 10588 2.96 - 3.45: 22544 3.45 - 3.93: 39814 3.93 - 4.42: 44218 4.42 - 4.90: 75715 Nonbonded interactions: 192879 Sorted by model distance: nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.478 3.040 nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.495 3.040 nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.510 3.040 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.516 3.040 nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.520 3.040 ... (remaining 192874 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.390 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.670 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.078 24435 Z= 0.770 Angle : 1.793 9.778 33312 Z= 1.199 Chirality : 0.096 0.407 3876 Planarity : 0.014 0.180 4251 Dihedral : 13.053 88.958 9168 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 0.08 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.35 % Favored : 94.42 % Rotamer: Outliers : 1.07 % Allowed : 2.36 % Favored : 96.57 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.14), residues: 2955 helix: -1.16 (0.16), residues: 670 sheet: -0.04 (0.21), residues: 574 loop : -0.87 (0.14), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1019 TYR 0.202 0.021 TYR B 28 PHE 0.080 0.012 PHE C 718 TRP 0.087 0.023 TRP B 104 HIS 0.009 0.002 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.01330 (24366) covalent geometry : angle 1.77819 (33144) SS BOND : bond 0.01482 ( 39) SS BOND : angle 2.29447 ( 78) hydrogen bonds : bond 0.14667 ( 1027) hydrogen bonds : angle 8.47982 ( 2835) link_NAG-ASN : bond 0.01124 ( 30) link_NAG-ASN : angle 4.60199 ( 90) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 449 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.6541 (p90) cc_final: 0.6062 (p90) REVERT: A 334 ASN cc_start: 0.8048 (m-40) cc_final: 0.7760 (m110) REVERT: A 396 TYR cc_start: 0.6137 (m-80) cc_final: 0.5898 (m-80) REVERT: A 408 ARG cc_start: 0.7910 (ptp-110) cc_final: 0.7631 (mpp80) REVERT: A 421 TYR cc_start: 0.6189 (m-10) cc_final: 0.5434 (m-10) REVERT: A 900 MET cc_start: 0.7855 (mtp) cc_final: 0.7631 (mtp) REVERT: A 985 ASP cc_start: 0.6894 (m-30) cc_final: 0.6459 (m-30) REVERT: B 323 THR cc_start: 0.7552 (m) cc_final: 0.7085 (p) REVERT: B 396 TYR cc_start: 0.6301 (m-80) cc_final: 0.5788 (m-80) REVERT: B 400 PHE cc_start: 0.6974 (p90) cc_final: 0.6709 (p90) REVERT: B 453 PHE cc_start: 0.7368 (p90) cc_final: 0.6976 (p90) REVERT: C 198 ASP cc_start: 0.7566 (m-30) cc_final: 0.7093 (m-30) REVERT: C 227 VAL cc_start: 0.7997 (m) cc_final: 0.7749 (m) REVERT: C 360 ASN cc_start: 0.7792 (m110) cc_final: 0.7338 (t0) REVERT: C 380 TYR cc_start: 0.8078 (m-80) cc_final: 0.7855 (m-80) REVERT: C 394 ASN cc_start: 0.6304 (m-40) cc_final: 0.6083 (m-40) REVERT: C 429 PHE cc_start: 0.7547 (t80) cc_final: 0.7148 (t80) REVERT: C 511 VAL cc_start: 0.8204 (t) cc_final: 0.8001 (m) REVERT: C 612 TYR cc_start: 0.8239 (m-80) cc_final: 0.8022 (m-80) REVERT: C 773 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7448 (pt0) REVERT: C 1142 GLN cc_start: 0.7675 (tp40) cc_final: 0.7348 (tp40) outliers start: 28 outliers final: 5 residues processed: 470 average time/residue: 0.1648 time to fit residues: 119.0373 Evaluate side-chains 248 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 242 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 773 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS A1088 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B 949 GLN C 52 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.181792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.128757 restraints weight = 35537.321| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.55 r_work: 0.3415 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24435 Z= 0.179 Angle : 0.724 12.055 33312 Z= 0.377 Chirality : 0.049 0.313 3876 Planarity : 0.004 0.035 4251 Dihedral : 6.674 64.203 3841 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.57 % Favored : 97.39 % Rotamer: Outliers : 1.83 % Allowed : 7.40 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.15), residues: 2955 helix: 0.46 (0.19), residues: 682 sheet: -0.00 (0.19), residues: 660 loop : -0.64 (0.15), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 237 TYR 0.030 0.002 TYR A 396 PHE 0.020 0.002 PHE C 338 TRP 0.021 0.002 TRP B 436 HIS 0.007 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00406 (24366) covalent geometry : angle 0.68813 (33144) SS BOND : bond 0.00537 ( 39) SS BOND : angle 1.88088 ( 78) hydrogen bonds : bond 0.04680 ( 1027) hydrogen bonds : angle 6.48276 ( 2835) link_NAG-ASN : bond 0.00385 ( 30) link_NAG-ASN : angle 4.07991 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 260 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 PHE cc_start: 0.6950 (t80) cc_final: 0.6556 (t80) REVERT: A 238 PHE cc_start: 0.6343 (p90) cc_final: 0.5782 (p90) REVERT: A 421 TYR cc_start: 0.6187 (m-10) cc_final: 0.5778 (m-10) REVERT: A 641 ASN cc_start: 0.6365 (t0) cc_final: 0.6092 (m110) REVERT: A 912 THR cc_start: 0.7845 (OUTLIER) cc_final: 0.7590 (p) REVERT: A 957 GLN cc_start: 0.8204 (tp40) cc_final: 0.7947 (tt0) REVERT: B 41 LYS cc_start: 0.8138 (mttt) cc_final: 0.7843 (mtpt) REVERT: B 129 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7722 (tttp) REVERT: B 323 THR cc_start: 0.7471 (m) cc_final: 0.7038 (p) REVERT: B 421 TYR cc_start: 0.6877 (m-10) cc_final: 0.5766 (m-80) REVERT: B 453 PHE cc_start: 0.7349 (p90) cc_final: 0.7101 (p90) REVERT: B 464 PHE cc_start: 0.7536 (m-10) cc_final: 0.6628 (m-10) REVERT: B 537 LYS cc_start: 0.7082 (ttpt) cc_final: 0.6117 (mmtm) REVERT: B 1135 ASN cc_start: 0.6781 (OUTLIER) cc_final: 0.6456 (m110) REVERT: C 132 GLU cc_start: 0.5214 (OUTLIER) cc_final: 0.4581 (pm20) REVERT: C 198 ASP cc_start: 0.7558 (m-30) cc_final: 0.7211 (t70) REVERT: C 328 ARG cc_start: 0.6932 (mmp-170) cc_final: 0.6673 (mmt-90) REVERT: C 360 ASN cc_start: 0.7497 (m110) cc_final: 0.7110 (t0) REVERT: C 394 ASN cc_start: 0.6781 (m-40) cc_final: 0.6402 (m-40) REVERT: C 396 TYR cc_start: 0.6353 (m-80) cc_final: 0.5907 (m-10) REVERT: C 418 ILE cc_start: 0.7654 (mm) cc_final: 0.7436 (tp) REVERT: C 429 PHE cc_start: 0.7619 (t80) cc_final: 0.7206 (t80) REVERT: C 512 VAL cc_start: 0.8434 (t) cc_final: 0.8074 (m) REVERT: C 546 LEU cc_start: 0.5668 (tt) cc_final: 0.5196 (mt) REVERT: C 790 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8427 (mtmm) REVERT: C 1050 MET cc_start: 0.7681 (ttp) cc_final: 0.7452 (ttm) outliers start: 48 outliers final: 22 residues processed: 295 average time/residue: 0.1511 time to fit residues: 70.9344 Evaluate side-chains 244 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 217 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1135 ASN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 790 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 52 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 256 optimal weight: 6.9990 chunk 272 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 chunk 246 optimal weight: 10.0000 chunk 281 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 214 optimal weight: 0.9990 chunk 140 optimal weight: 0.9990 chunk 229 optimal weight: 0.4980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 957 GLN C1010 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.182448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.129971 restraints weight = 35553.605| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.66 r_work: 0.3437 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24435 Z= 0.125 Angle : 0.598 11.073 33312 Z= 0.312 Chirality : 0.045 0.243 3876 Planarity : 0.004 0.041 4251 Dihedral : 5.809 52.576 3837 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.25 % Favored : 96.72 % Rotamer: Outliers : 1.91 % Allowed : 9.12 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.15), residues: 2955 helix: 1.26 (0.20), residues: 672 sheet: 0.07 (0.20), residues: 650 loop : -0.50 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 34 TYR 0.021 0.001 TYR A 265 PHE 0.019 0.001 PHE C 338 TRP 0.015 0.001 TRP B 436 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00272 (24366) covalent geometry : angle 0.57700 (33144) SS BOND : bond 0.00411 ( 39) SS BOND : angle 1.65443 ( 78) hydrogen bonds : bond 0.03860 ( 1027) hydrogen bonds : angle 5.91744 ( 2835) link_NAG-ASN : bond 0.00258 ( 30) link_NAG-ASN : angle 2.74557 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 254 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 PHE cc_start: 0.6877 (t80) cc_final: 0.6583 (t80) REVERT: A 238 PHE cc_start: 0.6307 (p90) cc_final: 0.5662 (p90) REVERT: A 360 ASN cc_start: 0.7962 (t0) cc_final: 0.7712 (t0) REVERT: A 421 TYR cc_start: 0.5989 (m-10) cc_final: 0.5623 (m-10) REVERT: A 641 ASN cc_start: 0.6334 (t0) cc_final: 0.6068 (m110) REVERT: B 41 LYS cc_start: 0.8176 (mttt) cc_final: 0.7842 (mtpt) REVERT: B 129 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7732 (tptp) REVERT: B 188 ASN cc_start: 0.5880 (m-40) cc_final: 0.5609 (m-40) REVERT: B 190 ARG cc_start: 0.7039 (mpt-90) cc_final: 0.6798 (mpt-90) REVERT: B 207 HIS cc_start: 0.7068 (t-90) cc_final: 0.6618 (t-90) REVERT: B 323 THR cc_start: 0.7456 (m) cc_final: 0.7016 (p) REVERT: B 326 ILE cc_start: 0.8037 (mm) cc_final: 0.7727 (pt) REVERT: B 453 PHE cc_start: 0.7342 (p90) cc_final: 0.7026 (p90) REVERT: B 464 PHE cc_start: 0.7460 (m-80) cc_final: 0.7166 (m-10) REVERT: B 537 LYS cc_start: 0.7037 (ttpt) cc_final: 0.6101 (mmtm) REVERT: C 347 PHE cc_start: 0.7186 (OUTLIER) cc_final: 0.6851 (m-10) REVERT: C 360 ASN cc_start: 0.7535 (m110) cc_final: 0.7116 (t0) REVERT: C 429 PHE cc_start: 0.7537 (t80) cc_final: 0.7287 (t80) REVERT: C 512 VAL cc_start: 0.8279 (t) cc_final: 0.7830 (m) REVERT: C 546 LEU cc_start: 0.5988 (tt) cc_final: 0.5668 (pp) REVERT: C 708 SER cc_start: 0.8475 (t) cc_final: 0.8130 (m) REVERT: C 790 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8480 (mtmm) REVERT: C 1142 GLN cc_start: 0.7906 (tp40) cc_final: 0.7548 (tp40) outliers start: 50 outliers final: 20 residues processed: 291 average time/residue: 0.1499 time to fit residues: 69.8439 Evaluate side-chains 232 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 209 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 245 optimal weight: 8.9990 chunk 157 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 204 optimal weight: 8.9990 chunk 200 optimal weight: 20.0000 chunk 262 optimal weight: 3.9990 chunk 243 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 145 optimal weight: 8.9990 chunk 299 optimal weight: 0.0000 chunk 93 optimal weight: 1.9990 overall best weight: 2.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 675 GLN B 66 HIS ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 957 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.178785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.124952 restraints weight = 35430.612| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.60 r_work: 0.3361 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 24435 Z= 0.262 Angle : 0.684 11.717 33312 Z= 0.352 Chirality : 0.050 0.653 3876 Planarity : 0.004 0.044 4251 Dihedral : 5.794 55.618 3831 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.82 % Favored : 96.14 % Rotamer: Outliers : 2.44 % Allowed : 9.92 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.15), residues: 2955 helix: 0.81 (0.20), residues: 662 sheet: -0.05 (0.20), residues: 636 loop : -0.67 (0.14), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 357 TYR 0.023 0.002 TYR C1067 PHE 0.028 0.002 PHE B1121 TRP 0.015 0.002 TRP B 436 HIS 0.006 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00625 (24366) covalent geometry : angle 0.66017 (33144) SS BOND : bond 0.00447 ( 39) SS BOND : angle 1.96890 ( 78) hydrogen bonds : bond 0.04417 ( 1027) hydrogen bonds : angle 6.15517 ( 2835) link_NAG-ASN : bond 0.00330 ( 30) link_NAG-ASN : angle 3.00982 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 224 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.6465 (p90) cc_final: 0.5862 (p90) REVERT: A 360 ASN cc_start: 0.8162 (t0) cc_final: 0.7933 (t0) REVERT: A 378 LYS cc_start: 0.7393 (tppt) cc_final: 0.7168 (tptp) REVERT: A 641 ASN cc_start: 0.6507 (t0) cc_final: 0.6133 (m110) REVERT: B 41 LYS cc_start: 0.8363 (mttt) cc_final: 0.8034 (mtpt) REVERT: B 129 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7822 (tptp) REVERT: B 190 ARG cc_start: 0.7236 (mpt-90) cc_final: 0.7000 (mpt-90) REVERT: B 207 HIS cc_start: 0.7046 (t-90) cc_final: 0.6504 (t-90) REVERT: B 323 THR cc_start: 0.7432 (m) cc_final: 0.6924 (p) REVERT: B 396 TYR cc_start: 0.6666 (m-80) cc_final: 0.6431 (m-80) REVERT: B 421 TYR cc_start: 0.7499 (m-10) cc_final: 0.6609 (m-80) REVERT: B 453 PHE cc_start: 0.7250 (p90) cc_final: 0.6916 (p90) REVERT: B 1135 ASN cc_start: 0.6968 (OUTLIER) cc_final: 0.6293 (m110) REVERT: C 198 ASP cc_start: 0.7543 (m-30) cc_final: 0.7224 (t70) REVERT: C 360 ASN cc_start: 0.7673 (m110) cc_final: 0.7103 (t0) REVERT: C 400 PHE cc_start: 0.6831 (p90) cc_final: 0.6559 (p90) REVERT: C 453 PHE cc_start: 0.6490 (p90) cc_final: 0.6195 (p90) REVERT: C 546 LEU cc_start: 0.5495 (tt) cc_final: 0.4995 (mt) REVERT: C 663 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.8035 (m-30) REVERT: C 708 SER cc_start: 0.8509 (t) cc_final: 0.8131 (m) REVERT: C 740 MET cc_start: 0.8965 (ttm) cc_final: 0.8721 (ttt) REVERT: C 790 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8451 (mtmm) REVERT: C 1142 GLN cc_start: 0.7884 (tp40) cc_final: 0.7669 (tp40) outliers start: 64 outliers final: 39 residues processed: 271 average time/residue: 0.1439 time to fit residues: 62.6326 Evaluate side-chains 249 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 206 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1135 ASN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 278 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 157 optimal weight: 0.8980 chunk 194 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 296 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 185 optimal weight: 0.7980 chunk 263 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.182094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.129149 restraints weight = 35300.651| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.59 r_work: 0.3422 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24435 Z= 0.118 Angle : 0.573 9.615 33312 Z= 0.298 Chirality : 0.045 0.292 3876 Planarity : 0.004 0.071 4251 Dihedral : 5.360 45.376 3831 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.01 % Favored : 96.95 % Rotamer: Outliers : 1.72 % Allowed : 11.10 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.15), residues: 2955 helix: 1.39 (0.21), residues: 664 sheet: 0.03 (0.20), residues: 629 loop : -0.57 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 237 TYR 0.022 0.001 TYR B 505 PHE 0.038 0.001 PHE C 338 TRP 0.017 0.001 TRP B 436 HIS 0.004 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00260 (24366) covalent geometry : angle 0.55270 (33144) SS BOND : bond 0.00353 ( 39) SS BOND : angle 1.93347 ( 78) hydrogen bonds : bond 0.03597 ( 1027) hydrogen bonds : angle 5.72217 ( 2835) link_NAG-ASN : bond 0.00304 ( 30) link_NAG-ASN : angle 2.38276 ( 90) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 229 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.6033 (m-80) cc_final: 0.5749 (m-80) REVERT: A 201 PHE cc_start: 0.7145 (t80) cc_final: 0.6704 (t80) REVERT: A 238 PHE cc_start: 0.6418 (p90) cc_final: 0.6088 (p90) REVERT: A 360 ASN cc_start: 0.8188 (t0) cc_final: 0.7874 (t0) REVERT: A 378 LYS cc_start: 0.7467 (tppt) cc_final: 0.7249 (tptp) REVERT: A 390 LEU cc_start: 0.7730 (mt) cc_final: 0.7474 (mt) REVERT: A 641 ASN cc_start: 0.6381 (t0) cc_final: 0.6054 (m110) REVERT: A 869 MET cc_start: 0.8795 (mtt) cc_final: 0.8564 (mtm) REVERT: B 41 LYS cc_start: 0.8247 (mttt) cc_final: 0.7932 (mtpt) REVERT: B 129 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.8049 (tptp) REVERT: B 190 ARG cc_start: 0.7118 (mpt-90) cc_final: 0.6892 (mpt-90) REVERT: B 207 HIS cc_start: 0.7138 (t-90) cc_final: 0.6521 (t-90) REVERT: B 323 THR cc_start: 0.7445 (m) cc_final: 0.6983 (p) REVERT: B 326 ILE cc_start: 0.8099 (mm) cc_final: 0.7806 (pt) REVERT: B 378 LYS cc_start: 0.7323 (ttmt) cc_final: 0.7051 (ttmt) REVERT: B 396 TYR cc_start: 0.6694 (m-80) cc_final: 0.6199 (m-80) REVERT: B 421 TYR cc_start: 0.7330 (m-10) cc_final: 0.6403 (m-80) REVERT: B 453 PHE cc_start: 0.7225 (p90) cc_final: 0.6944 (p90) REVERT: C 198 ASP cc_start: 0.7532 (m-30) cc_final: 0.7006 (t70) REVERT: C 200 TYR cc_start: 0.7384 (m-80) cc_final: 0.7092 (m-80) REVERT: C 360 ASN cc_start: 0.7676 (m110) cc_final: 0.7220 (t0) REVERT: C 429 PHE cc_start: 0.7156 (t80) cc_final: 0.6553 (t80) REVERT: C 453 PHE cc_start: 0.6663 (p90) cc_final: 0.6329 (p90) REVERT: C 546 LEU cc_start: 0.5292 (tt) cc_final: 0.4888 (mt) REVERT: C 576 VAL cc_start: 0.7171 (t) cc_final: 0.6894 (t) REVERT: C 603 ASN cc_start: 0.7521 (t0) cc_final: 0.7195 (t0) REVERT: C 708 SER cc_start: 0.8307 (t) cc_final: 0.8004 (m) outliers start: 45 outliers final: 28 residues processed: 261 average time/residue: 0.1529 time to fit residues: 64.7780 Evaluate side-chains 235 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 206 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 170 optimal weight: 4.9990 chunk 144 optimal weight: 0.0170 chunk 210 optimal weight: 0.0050 chunk 104 optimal weight: 0.9980 chunk 213 optimal weight: 7.9990 chunk 216 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 25 optimal weight: 0.4980 chunk 280 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 overall best weight: 1.1034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 856 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.180878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.128206 restraints weight = 35536.795| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.51 r_work: 0.3422 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24435 Z= 0.130 Angle : 0.561 9.417 33312 Z= 0.291 Chirality : 0.045 0.321 3876 Planarity : 0.003 0.042 4251 Dihedral : 5.103 43.312 3831 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.28 % Favored : 96.68 % Rotamer: Outliers : 1.79 % Allowed : 11.90 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.15), residues: 2955 helix: 1.46 (0.20), residues: 665 sheet: 0.06 (0.19), residues: 645 loop : -0.52 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 237 TYR 0.026 0.001 TYR B 505 PHE 0.019 0.001 PHE C 338 TRP 0.015 0.001 TRP B 436 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00297 (24366) covalent geometry : angle 0.54217 (33144) SS BOND : bond 0.00346 ( 39) SS BOND : angle 2.01686 ( 78) hydrogen bonds : bond 0.03618 ( 1027) hydrogen bonds : angle 5.67602 ( 2835) link_NAG-ASN : bond 0.00291 ( 30) link_NAG-ASN : angle 2.20488 ( 90) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 215 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7048 (ttp-110) cc_final: 0.6785 (ttp-110) REVERT: A 360 ASN cc_start: 0.8239 (t0) cc_final: 0.7777 (t0) REVERT: A 390 LEU cc_start: 0.7872 (mt) cc_final: 0.7588 (mt) REVERT: A 560 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7973 (mt) REVERT: A 568 ASP cc_start: 0.6861 (t0) cc_final: 0.6634 (t0) REVERT: A 581 THR cc_start: 0.8230 (OUTLIER) cc_final: 0.8025 (p) REVERT: A 641 ASN cc_start: 0.6521 (t0) cc_final: 0.6212 (m110) REVERT: A 796 ASP cc_start: 0.6415 (p0) cc_final: 0.6180 (p0) REVERT: B 41 LYS cc_start: 0.8259 (mttt) cc_final: 0.7951 (mtpt) REVERT: B 129 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.8116 (tptp) REVERT: B 190 ARG cc_start: 0.7131 (mpt-90) cc_final: 0.6906 (mpt-90) REVERT: B 207 HIS cc_start: 0.7143 (t-90) cc_final: 0.6385 (t-90) REVERT: B 323 THR cc_start: 0.7473 (m) cc_final: 0.7004 (p) REVERT: B 326 ILE cc_start: 0.8175 (mm) cc_final: 0.7882 (pt) REVERT: B 378 LYS cc_start: 0.7254 (ttmt) cc_final: 0.6867 (mtmt) REVERT: B 396 TYR cc_start: 0.6735 (m-80) cc_final: 0.6249 (m-80) REVERT: B 421 TYR cc_start: 0.7329 (m-10) cc_final: 0.6343 (m-80) REVERT: B 453 PHE cc_start: 0.7045 (p90) cc_final: 0.6821 (p90) REVERT: C 198 ASP cc_start: 0.7567 (m-30) cc_final: 0.7139 (t70) REVERT: C 360 ASN cc_start: 0.7901 (m110) cc_final: 0.7241 (t0) REVERT: C 453 PHE cc_start: 0.6456 (p90) cc_final: 0.6186 (p90) REVERT: C 546 LEU cc_start: 0.5253 (tt) cc_final: 0.4838 (mt) REVERT: C 576 VAL cc_start: 0.7190 (t) cc_final: 0.6937 (t) REVERT: C 603 ASN cc_start: 0.7470 (t0) cc_final: 0.7159 (t0) REVERT: C 708 SER cc_start: 0.8263 (t) cc_final: 0.7981 (m) outliers start: 47 outliers final: 28 residues processed: 249 average time/residue: 0.1414 time to fit residues: 57.0691 Evaluate side-chains 233 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 202 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 236 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 209 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 154 optimal weight: 0.7980 chunk 217 optimal weight: 10.0000 chunk 203 optimal weight: 2.9990 chunk 216 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 69 optimal weight: 0.0770 overall best weight: 2.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN C 207 HIS C1010 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.178595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.124825 restraints weight = 35323.816| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.63 r_work: 0.3354 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 24435 Z= 0.242 Angle : 0.649 9.449 33312 Z= 0.335 Chirality : 0.048 0.337 3876 Planarity : 0.004 0.046 4251 Dihedral : 5.384 44.522 3831 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.06 % Favored : 95.91 % Rotamer: Outliers : 2.02 % Allowed : 11.82 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.15), residues: 2955 helix: 1.04 (0.20), residues: 659 sheet: 0.08 (0.20), residues: 629 loop : -0.77 (0.14), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 237 TYR 0.028 0.002 TYR B 505 PHE 0.027 0.002 PHE A1121 TRP 0.015 0.002 TRP B 436 HIS 0.006 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00579 (24366) covalent geometry : angle 0.62737 (33144) SS BOND : bond 0.00417 ( 39) SS BOND : angle 2.39645 ( 78) hydrogen bonds : bond 0.04189 ( 1027) hydrogen bonds : angle 6.00081 ( 2835) link_NAG-ASN : bond 0.00306 ( 30) link_NAG-ASN : angle 2.42011 ( 90) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 217 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8000 (m-80) cc_final: 0.7493 (m-10) REVERT: A 237 ARG cc_start: 0.7109 (ttp-110) cc_final: 0.6801 (ttp-110) REVERT: A 360 ASN cc_start: 0.8302 (t0) cc_final: 0.7853 (t0) REVERT: B 41 LYS cc_start: 0.8383 (mttt) cc_final: 0.8092 (mtpt) REVERT: B 190 ARG cc_start: 0.7188 (mpt-90) cc_final: 0.6939 (mpt-90) REVERT: B 207 HIS cc_start: 0.6992 (t-90) cc_final: 0.6368 (t-90) REVERT: B 284 THR cc_start: 0.8344 (p) cc_final: 0.8010 (t) REVERT: B 323 THR cc_start: 0.7460 (m) cc_final: 0.6954 (p) REVERT: B 326 ILE cc_start: 0.8178 (mm) cc_final: 0.7950 (pt) REVERT: B 378 LYS cc_start: 0.7334 (ttmt) cc_final: 0.6984 (mtmt) REVERT: B 380 TYR cc_start: 0.7934 (m-80) cc_final: 0.7521 (m-10) REVERT: B 400 PHE cc_start: 0.6731 (p90) cc_final: 0.6499 (p90) REVERT: B 421 TYR cc_start: 0.7169 (m-10) cc_final: 0.6296 (m-80) REVERT: C 198 ASP cc_start: 0.7565 (m-30) cc_final: 0.7318 (t70) REVERT: C 347 PHE cc_start: 0.7079 (m-10) cc_final: 0.6198 (m-10) REVERT: C 360 ASN cc_start: 0.7692 (m110) cc_final: 0.7257 (t0) REVERT: C 429 PHE cc_start: 0.7374 (t80) cc_final: 0.6806 (t80) REVERT: C 453 PHE cc_start: 0.6130 (p90) cc_final: 0.5876 (p90) REVERT: C 546 LEU cc_start: 0.5479 (tt) cc_final: 0.5016 (mt) REVERT: C 576 VAL cc_start: 0.7254 (t) cc_final: 0.6993 (t) REVERT: C 663 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.8092 (m-30) REVERT: C 708 SER cc_start: 0.8388 (t) cc_final: 0.8036 (m) outliers start: 53 outliers final: 44 residues processed: 257 average time/residue: 0.1412 time to fit residues: 59.0861 Evaluate side-chains 247 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 202 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 66 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 chunk 276 optimal weight: 0.6980 chunk 242 optimal weight: 10.0000 chunk 287 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS B 957 GLN C 207 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.179516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.122645 restraints weight = 34960.503| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.45 r_work: 0.3372 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 24435 Z= 0.149 Angle : 0.582 11.267 33312 Z= 0.300 Chirality : 0.045 0.365 3876 Planarity : 0.003 0.043 4251 Dihedral : 5.128 44.555 3831 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.55 % Favored : 96.41 % Rotamer: Outliers : 1.79 % Allowed : 12.40 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.15), residues: 2955 helix: 1.33 (0.20), residues: 662 sheet: 0.11 (0.20), residues: 630 loop : -0.71 (0.15), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 408 TYR 0.018 0.001 TYR B 369 PHE 0.021 0.001 PHE C 168 TRP 0.016 0.001 TRP B 436 HIS 0.004 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00350 (24366) covalent geometry : angle 0.56146 (33144) SS BOND : bond 0.00336 ( 39) SS BOND : angle 2.23450 ( 78) hydrogen bonds : bond 0.03672 ( 1027) hydrogen bonds : angle 5.74606 ( 2835) link_NAG-ASN : bond 0.00237 ( 30) link_NAG-ASN : angle 2.22427 ( 90) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 215 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7140 (ttp-110) cc_final: 0.6804 (ttp-110) REVERT: A 360 ASN cc_start: 0.8437 (t0) cc_final: 0.8037 (t0) REVERT: B 41 LYS cc_start: 0.8292 (mttt) cc_final: 0.7822 (mtpt) REVERT: B 190 ARG cc_start: 0.6890 (mpt-90) cc_final: 0.6583 (mpt-90) REVERT: B 207 HIS cc_start: 0.6857 (t-90) cc_final: 0.6180 (t-90) REVERT: B 216 LEU cc_start: 0.7036 (OUTLIER) cc_final: 0.6753 (tt) REVERT: B 323 THR cc_start: 0.7385 (m) cc_final: 0.6902 (p) REVERT: B 326 ILE cc_start: 0.8001 (mm) cc_final: 0.7685 (pt) REVERT: B 378 LYS cc_start: 0.7077 (ttmt) cc_final: 0.6779 (mtmt) REVERT: B 380 TYR cc_start: 0.7578 (m-80) cc_final: 0.7206 (m-10) REVERT: B 421 TYR cc_start: 0.6979 (m-10) cc_final: 0.6200 (m-80) REVERT: B 571 ASP cc_start: 0.7892 (OUTLIER) cc_final: 0.7014 (t0) REVERT: C 80 ASP cc_start: 0.5488 (t0) cc_final: 0.4588 (m-30) REVERT: C 198 ASP cc_start: 0.7518 (m-30) cc_final: 0.7139 (t70) REVERT: C 360 ASN cc_start: 0.7657 (m110) cc_final: 0.7241 (t0) REVERT: C 429 PHE cc_start: 0.7291 (t80) cc_final: 0.6816 (t80) REVERT: C 453 PHE cc_start: 0.6391 (p90) cc_final: 0.6110 (p90) REVERT: C 523 THR cc_start: 0.8072 (p) cc_final: 0.7712 (p) REVERT: C 546 LEU cc_start: 0.5111 (tt) cc_final: 0.4674 (mt) REVERT: C 576 VAL cc_start: 0.7182 (t) cc_final: 0.6949 (t) REVERT: C 708 SER cc_start: 0.8330 (t) cc_final: 0.7954 (m) outliers start: 47 outliers final: 37 residues processed: 250 average time/residue: 0.1432 time to fit residues: 58.5904 Evaluate side-chains 245 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 206 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 23 optimal weight: 10.0000 chunk 286 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 170 optimal weight: 4.9990 chunk 209 optimal weight: 9.9990 chunk 152 optimal weight: 1.9990 chunk 294 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 155 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.179260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.124981 restraints weight = 35058.187| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.75 r_work: 0.3379 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24435 Z= 0.145 Angle : 0.576 11.167 33312 Z= 0.295 Chirality : 0.046 0.390 3876 Planarity : 0.003 0.043 4251 Dihedral : 5.061 43.783 3831 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.82 % Favored : 96.14 % Rotamer: Outliers : 1.83 % Allowed : 12.43 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.15), residues: 2955 helix: 1.39 (0.20), residues: 670 sheet: 0.10 (0.19), residues: 648 loop : -0.68 (0.15), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 408 TYR 0.027 0.001 TYR B 505 PHE 0.024 0.001 PHE C 168 TRP 0.015 0.001 TRP B 436 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00339 (24366) covalent geometry : angle 0.55638 (33144) SS BOND : bond 0.00303 ( 39) SS BOND : angle 2.01932 ( 78) hydrogen bonds : bond 0.03614 ( 1027) hydrogen bonds : angle 5.67694 ( 2835) link_NAG-ASN : bond 0.00267 ( 30) link_NAG-ASN : angle 2.25272 ( 90) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 215 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7933 (m-80) cc_final: 0.7405 (m-10) REVERT: A 216 LEU cc_start: 0.7373 (mp) cc_final: 0.7166 (mp) REVERT: A 237 ARG cc_start: 0.7107 (ttp-110) cc_final: 0.6768 (ttp-110) REVERT: A 360 ASN cc_start: 0.8495 (t0) cc_final: 0.8112 (t0) REVERT: B 41 LYS cc_start: 0.8299 (mttt) cc_final: 0.7823 (mtpt) REVERT: B 190 ARG cc_start: 0.6863 (mpt-90) cc_final: 0.6569 (mpt-90) REVERT: B 207 HIS cc_start: 0.6860 (t-90) cc_final: 0.6190 (t-90) REVERT: B 216 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6658 (tt) REVERT: B 323 THR cc_start: 0.7458 (m) cc_final: 0.6980 (p) REVERT: B 326 ILE cc_start: 0.8007 (mm) cc_final: 0.7715 (pt) REVERT: B 378 LYS cc_start: 0.7061 (ttmt) cc_final: 0.6777 (mtmt) REVERT: B 380 TYR cc_start: 0.7557 (m-80) cc_final: 0.7204 (m-10) REVERT: B 421 TYR cc_start: 0.7033 (m-10) cc_final: 0.6280 (m-80) REVERT: B 453 PHE cc_start: 0.6738 (p90) cc_final: 0.6440 (p90) REVERT: B 537 LYS cc_start: 0.6989 (ttpt) cc_final: 0.6235 (mmtm) REVERT: B 569 ILE cc_start: 0.8626 (mp) cc_final: 0.8421 (pt) REVERT: B 571 ASP cc_start: 0.7903 (OUTLIER) cc_final: 0.7199 (t0) REVERT: C 80 ASP cc_start: 0.5512 (t0) cc_final: 0.4701 (m-30) REVERT: C 198 ASP cc_start: 0.7558 (m-30) cc_final: 0.7168 (t70) REVERT: C 360 ASN cc_start: 0.7667 (m110) cc_final: 0.7329 (t0) REVERT: C 429 PHE cc_start: 0.7365 (t80) cc_final: 0.6924 (t80) REVERT: C 453 PHE cc_start: 0.6201 (p90) cc_final: 0.5944 (p90) REVERT: C 546 LEU cc_start: 0.5067 (tt) cc_final: 0.4617 (mt) REVERT: C 565 PHE cc_start: 0.7645 (m-10) cc_final: 0.7411 (m-10) REVERT: C 576 VAL cc_start: 0.7142 (t) cc_final: 0.6843 (t) REVERT: C 663 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.8123 (m-30) REVERT: C 708 SER cc_start: 0.8310 (t) cc_final: 0.8021 (m) outliers start: 48 outliers final: 40 residues processed: 251 average time/residue: 0.1404 time to fit residues: 57.3075 Evaluate side-chains 250 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 207 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 132 optimal weight: 0.1980 chunk 19 optimal weight: 0.9980 chunk 124 optimal weight: 0.0870 chunk 213 optimal weight: 0.9990 chunk 205 optimal weight: 10.0000 chunk 39 optimal weight: 20.0000 chunk 176 optimal weight: 0.6980 chunk 20 optimal weight: 0.0030 chunk 183 optimal weight: 0.9980 chunk 136 optimal weight: 0.0770 chunk 182 optimal weight: 2.9990 overall best weight: 0.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.182830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.132525 restraints weight = 35393.937| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.81 r_work: 0.3425 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 24435 Z= 0.094 Angle : 0.530 11.539 33312 Z= 0.272 Chirality : 0.044 0.378 3876 Planarity : 0.003 0.042 4251 Dihedral : 4.609 41.021 3831 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.07 % Allowed : 13.12 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.15), residues: 2955 helix: 1.81 (0.21), residues: 665 sheet: 0.26 (0.20), residues: 613 loop : -0.53 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 237 TYR 0.019 0.001 TYR B 369 PHE 0.025 0.001 PHE C 168 TRP 0.015 0.001 TRP B 436 HIS 0.006 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00198 (24366) covalent geometry : angle 0.51461 (33144) SS BOND : bond 0.00218 ( 39) SS BOND : angle 1.79905 ( 78) hydrogen bonds : bond 0.03190 ( 1027) hydrogen bonds : angle 5.34910 ( 2835) link_NAG-ASN : bond 0.00325 ( 30) link_NAG-ASN : angle 1.94833 ( 90) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 234 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7096 (ttp-110) cc_final: 0.6893 (ttp-110) REVERT: A 360 ASN cc_start: 0.8523 (t0) cc_final: 0.8144 (t0) REVERT: A 378 LYS cc_start: 0.7383 (tppt) cc_final: 0.7104 (tptp) REVERT: A 408 ARG cc_start: 0.8061 (ptp90) cc_final: 0.7695 (mpp80) REVERT: A 721 SER cc_start: 0.8592 (m) cc_final: 0.8367 (p) REVERT: A 858 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8641 (mp) REVERT: B 41 LYS cc_start: 0.8192 (mttt) cc_final: 0.7692 (mtpt) REVERT: B 207 HIS cc_start: 0.6910 (t-90) cc_final: 0.6234 (t-90) REVERT: B 216 LEU cc_start: 0.6699 (OUTLIER) cc_final: 0.6184 (tt) REVERT: B 271 GLN cc_start: 0.7410 (mm-40) cc_final: 0.6972 (mp10) REVERT: B 323 THR cc_start: 0.7329 (m) cc_final: 0.6867 (p) REVERT: B 326 ILE cc_start: 0.8074 (mm) cc_final: 0.7639 (pt) REVERT: B 378 LYS cc_start: 0.6978 (ttmt) cc_final: 0.6714 (mtmt) REVERT: B 380 TYR cc_start: 0.7509 (m-80) cc_final: 0.7168 (m-10) REVERT: B 421 TYR cc_start: 0.7022 (m-10) cc_final: 0.6216 (m-80) REVERT: B 453 PHE cc_start: 0.6686 (p90) cc_final: 0.6389 (p90) REVERT: B 537 LYS cc_start: 0.6938 (ttpt) cc_final: 0.6201 (mmtm) REVERT: B 571 ASP cc_start: 0.7726 (m-30) cc_final: 0.7049 (t0) REVERT: C 80 ASP cc_start: 0.5513 (t0) cc_final: 0.4715 (m-30) REVERT: C 198 ASP cc_start: 0.7539 (m-30) cc_final: 0.7030 (t70) REVERT: C 347 PHE cc_start: 0.7238 (m-10) cc_final: 0.6466 (m-10) REVERT: C 360 ASN cc_start: 0.7639 (m110) cc_final: 0.7421 (t0) REVERT: C 453 PHE cc_start: 0.6376 (p90) cc_final: 0.6111 (p90) REVERT: C 512 VAL cc_start: 0.8079 (t) cc_final: 0.7601 (m) REVERT: C 546 LEU cc_start: 0.5342 (tt) cc_final: 0.4851 (mt) REVERT: C 576 VAL cc_start: 0.7111 (t) cc_final: 0.6839 (t) outliers start: 28 outliers final: 19 residues processed: 253 average time/residue: 0.1454 time to fit residues: 60.2085 Evaluate side-chains 229 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 208 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 68 optimal weight: 0.9990 chunk 141 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 234 optimal weight: 10.0000 chunk 130 optimal weight: 0.9990 chunk 96 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 230 optimal weight: 10.0000 chunk 182 optimal weight: 3.9990 chunk 261 optimal weight: 0.4980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.180967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.128834 restraints weight = 35004.112| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.85 r_work: 0.3397 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24435 Z= 0.128 Angle : 0.552 11.609 33312 Z= 0.283 Chirality : 0.045 0.360 3876 Planarity : 0.003 0.043 4251 Dihedral : 4.626 40.161 3831 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.07 % Allowed : 13.88 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.15), residues: 2955 helix: 1.73 (0.20), residues: 671 sheet: 0.26 (0.20), residues: 638 loop : -0.51 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 237 TYR 0.028 0.001 TYR B 505 PHE 0.023 0.001 PHE C 168 TRP 0.013 0.001 TRP B 436 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00297 (24366) covalent geometry : angle 0.53490 (33144) SS BOND : bond 0.00256 ( 39) SS BOND : angle 2.00461 ( 78) hydrogen bonds : bond 0.03384 ( 1027) hydrogen bonds : angle 5.44536 ( 2835) link_NAG-ASN : bond 0.00259 ( 30) link_NAG-ASN : angle 1.93626 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7693.41 seconds wall clock time: 131 minutes 40.25 seconds (7900.25 seconds total)